How to skip reading the first line of an input file in Python

Question

I'm trying to write a script that will automatically process the files containing DNA sequences and convert them into a protein sequence. My only hiccup thus far is that in order for my script to process the infile I need to somehow omit the first line.

My code looks like this:

#!/usr/bin/python

### This script will translate in all three frames ###

import glob
from Bio.Seq import *
from Bio.Alphabet import generic_dna

print "Please drag in the directory to be processed: "
folder = raw_input().replace(" ","")
file = glob.glob(str(folder) + "/" + '*.seq')

for i in file:

        with open (i, "r") as myfile:

                ### Need to somehow remove / read over the first line of the input...###

                seq = myfile.read().replace(" ", "").replace("\n", "")

        x = 0

        output = open(i + ".tran", "w+")

        while x < 3:
                cd = Seq(seq[x:], generic_dna)
                qes = seq[::-1]
                cdr = Seq(qes[x:], generic_dna)
                error = cd.translate().count('*')
                reverror = cdr.translate().count('*')
                output.write(str(cd.translate()) + "\nStops: " + str(error) + "\n\n")
                output.write("Reverse\n" + str(cdr.translate()) + "\nStops: " + str(reverror) + "\n\n")
                x += 1

And my input files might look something like this

>G2-pBAD-Forward_A11.ab1
NNNNNNNNNNCNNNCNGNNGCTTTTTATCGCAACTCTCTACTGTTTCTCCATACCCGTTTTTTTGGGCTAGCGAATTCGA
GCTCGAAATAATTTTGTTTAACTTTAAGAAGGAGATATACATATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGT
ACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCAAGCTTGGCTGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACA
GATTAAATCAGAACGCAGAAGCGGTCTGATAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCA
TGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCA
TCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTA
GGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACT
GCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTTTGTTTATTTTTCT
AAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATG
AGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCT
GGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCAGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCA
ACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGGTTTATT
GCTGATAAATCTGGAGCCGGTGAGCGTGNTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTTCCCGTAT
CGNANTTNNCTACACGAN

What I need is an elegant way to remove that first line containing the '>'.

Answer 1

You can use SeqIO:

with open(i) as myfile:
    for record in SeqIO.parse(myfile, "fasta"):
       print record.id
       print record.seq  

record.seq will give you the sequence, record.id will give you the id, if you only have or want a single sequence in each you can just call next:

with open(i) as myfile:
    print(next(SeqIO.parse(myfile, "fasta"))).seq

I don't see any spaces in your input so I am not sure how replace would work, this will output the sequence as a single string.

Output:

NNNNNNNNNNCNNNCNGNNGCTTTTTATCGCAACTCTCTACTGTTTCTCCATACCCGTTTTTTTGGGCTAGCGAATTCGAGCTCGAAATAATTTTGTTTAACTTTAAGAAGGAGATATACATATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCAAGCTTGGCTGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCAGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGNTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTTCCCGTATCGNANTTNNCTACACGAN

You can also use range instead of your while loop and pass the alphabet to SeQIO:

for record in SeqIO.parse(myfile, "fasta",generic_dna)
    ...
for x in range(3):
       ....

This should be closer to what you want:

from Bio import SeqIO
from Bio.Alphabet import generic_dna
from Bio.Seq import Seq


folder = raw_input().replace(" ","")
files = glob.glob(folder + "/" + '*.seq')

for i in files:
    with open(i) as myfile:
            seq = next(SeqIO.parse(myfile, "fasta", generic_dna)).seq
            qes = seq[::-1]
            with open("{}.tran".format(i), "w+") as output:
                 for x in range(3):
                     cd = seq[x:]
                     cdr = qes[x:]
                     error = seq.translate().count('*')
                     reverror = cdr.translate().count('*')
                     output.write("{}\nstops: {}\n\n".format(cd.translate(), error))
                     output.write("Reverse: {}\nStops: {}\n\n ".format(cdr.translate(), reverror))

Which outputs:

XXXXXXXFLSQLSTVSPYPFFWASEFELEIILFNFKKEIYI*L**NELLPCLLYC*WAGR*MPGQAWLFWRMREDFQPDTD*IRTQKRSDKTEFAWRQ*RGGPT*PHAELRSETP*RRW*CGVSPCESRELPGIK*NERLSRKTGPFVLSVVCR*TLS*VGQIRRERI*TLRSNGPEGGGQDARHKLPGIKLSRRPS*RMAFLRFYKLFCLFF*IHSNMYPLMRQ*P**MLQ*Y*KRKSMSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGAANY*LANYLL*LPGNN**TGWRRIKLQDHFCARPFRLAGFIADKSGAGERXLAVSLQHWGQMVSPSRIXXXYT
stops: 25

Reverse: XHIXXXYALPEW*TGVTTLLWRSXASGRGLNSRYLGRSAFPARVFTRTLK*AEVGQIINNGPSISFIKRSIIKRRGLTRSRRK*KWSQRPTRFCPSVLRRFFPYSRCAFTTYEYEKEKVIITS*IVPITEYSPMYKLT*IFLFVFSNIFAFFR*AVLPEDELNYGPSNTARRTGGGRPGNEALQV*ARAA*TG*VLSQVAVCCLFCFPGQKADSESKINYGPSRDESVPLWGVMVAAMPQSEDSSRTPVHPGGAMTAVRLRQNSLAKTQD*IRHSPTFRRE*AVLSVRTGP*MAGRVVVMSFVPLLSKVMLVYI*RKNFNLF**SSSLSDRVFLPIPLCHLSTLFFXXXXXX
Stops: 15

 XXXXXXAFYRNSLLFLHTRFFGLANSSSK*FCLTLRRRYTYDCNETSYYPVCCTADGLVGKCLVKLGCFGG*EKIFSLIQIKSERRSGLIKQNLPGGSSAVVPPDPMPNSEVKRRSADGSVGSPHARVGNCQASNKTKGSVERLGLSFYLLFVGERSPE*DKSAGSGFERCEATARRVAGRTPAINCQASN*AEGHPDGWPFCVSTNSFVYFSKYIQICIRS*DNNPDKCFNNIEKGRV*VFNISVSPLFPFLRHFAFLFLLTQKRW*K*KMLKISWVQQTINWRTTYSSFPATINRLDGGG*SCRTTSALGPSGWLGLLLINLEPVSVXSRYHCSTGARW*ALPVSXXXTR
stops: 25

Reverse: STSXXAMPFPNGRPGSRRYYGALVRVAEV*IVVIWVGRPSRLASSPGR*NRRR*VR*LTTALRSHSSSGQLSNDVG*LEVVENESGRKDPLVFVLPFYGVFSLIPAVPLQLMSMRRKKL**LRK*SQ*QSTRLCINLHKSFYLFSQTSLRFSGRQSYRKTN*TTDRQIPPAGRAVGGPATKRCKFRRGPPKQDESSRKWLFVVYFAFRVRKLTRKAK*TTDRQGMRAYPSGV*W*PRCRKVKTQAVPQSTLVAR*RRSV*DKIVWRRRKTKLDIVRLLEESRRFCRFELVRKWLVG*SSCRLSHY*AK*C*YTYRGRISICFNKARA*AIGFFCPYLFVISQRYFSXXXXXX
Stops: 20

 XXXXXXLFIATLYCFSIPVFLG*RIRARNNFV*L*EGDIHMIVMKRVITLFAVLLMGWSVNAWSSLAVLADERRFSA*YRLNQNAEAV**NRICLAAVARWSHLTPCRTQK*NAVAPMVVWGLPMRE*GTARHQIKRKAQSKDWAFRFICCLSVNALLSRTNPPGADLNVAKQRPGGWRAGRPP*TARHQIKQKAILTDGLFAFLQTLLFIFLNTFKYVSAHETITLINASIILKKEEYEYSTFPCRPYSLFCGILPSCFCSPRNAGESKRC*RSVGCSKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWVYC**IWSR*AXSRGIIAALGPDGKPFPYRXXLHX
stops: 25

Reverse: AHXXXLCPSRMVDRGHDVTMALXCEWPRSK*SLFGSVGLPGSRLHQDVEIGGGRSDN*QRPFDLIHQAVNYQTTWVD*KS*KMKVVAKTHSFLSFRFTAFFPLFPLCLYNL*V*EGKSYNNFVNSPNNRVLAYV*TYINLFICFLKHLCVFPVGSPTGRRIKLRTVKYRPQDGRWEARQRSVASLGEGRLNRMSPLASGCLLSILLSGSES*LGKQNKLRTVKG*ERTPLGCDGSRDAAK*RLKPYPSPPWWRDDGGPFKTK*SGEDARLN*T*SDF*KRVGGFVGSNWSVNGWSGSRHVVCPIIEQSNVSIHIEEEFQFVLIKLELKRSGFFAHTSLSSLNAIFRXXXXXX
Stops: 14

Although there is a warning because your sequences are not a multiple of three

Answer 2

When you go to read the file check to see if the first character of the line is '>'. If it is then just read the line and skip it. Like the comment above mentioned, you may want to check this each time you read a line so you know if you are dealing with a new sequence or the same sequence, as your file may have multiple sequences.

This link will give you all of the documentation on reading a file in python. https://docs.python.org/2/tutorial/inputoutput.html

Answer 3

starting = True
lines = []
with open (i, "r") as myfile:
    for line in myfile:
        if starting:
            starting = False
            continue
        lines.append(line)

# now you have all the lines except the first one in "lines"