CODEWITHSUNDEEP
pythonstringpandaslistdataframe
lp97
lp97

Reputation: 75

Iteratively add new string as element in list

I am working with a data frame which consists of a column with numbers in the format: [[45, 45, 'D'],[46, 49, 'C'],[50, 66, 'S'],[67, 101, 'C'],[102, 103, 'S'],[104, 106, 'C'],[107, 108, 'S'],[109, 120, 'C'],[121, 121, 'S'],[122, 123, 'C'],[124, 140, 'S'],[141, 149, 'C'],[150, 176, 'S'],[177, 178, 'C'],[179, 181, 'S'],[182, 194, 'C'],[195, 213, 'S'],[214, 21``7, 'C']]

These numbers correspond to the positions of characters in a string: i.e. the string: 'MGILSFLPVLATESDWADCKSPQPWGHMLLWTAVLFLAPVAGTPAAPPKAVLKLEPQWINVLQEDSVTLTCRGTHSPESDSIQWFHNGNLIPTHTQPSYRFKANNNDSGEYTCQTGQTSLSDPVHLTVLSEWLVLQTPHLEFQEGETIVLRCHSWKDKPLVKVTFFQNGKSKKFSRSDPNFSIPQANHSHSGDYHCTGNIGYTLYSSKPVTITVQAPSSSPMGIIVAVVTGIAVAAIVAAVVALIYCRKKRISALPGYPECREMGETLPEKPANPTNPDEADKVGAENTITYSLLMHPDALEEPDDQNRI'

As you can see, some of the characters in the list are not corresponding to a number in the number list (i.e.) 0-44 is missing. So the characters at the 0-44th position have to be removed to create a shorter sequence of letters.

I am able to do this for one line, but I am struggling to do it for every line in the data frame.

This is the code for doing it for one line: 

new_s = ''

for item in res:
    new_s += strSeq[item[0]-1:item[1]]

print(len(new_s), new_s)

And this is what I have been trying to try to get it for all lines: 

shortenedSeq_list =[] 
counter=0
stringstring=[]
for rows in df.itertuples():
    strSeq2 = [rows.sequence]
    strremove2 = [rows.shortened_mobidb_consensus]
    for item in strremove2:
        res = ast.literal_eval(item)
    for item in res:
        stringstring.append(strSeq2[item[0]-1:item[1]])

stringstring

But this results in the output : 

 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 ['MGKGKPRGLNSARKLRVHRRNNRWAETTYKKRLLGTAFKSSPFGGSSHAKGIVLEKIGIESKQPNSAIRKCVRVQLIKNGKKVTAFVPNDGCLNFVDENDEVLLAGFGRKGKAKGDIPGVRFKVVKVSGVSLLALWKEKKEKPRS'],
 [],
 [],

Whereas I want each line in the list to be the sequence which has been shortened.

I ultimately want to add this list as a column in a the dataframe.

UPDATE

The numbers are outputted as a string rather than a list, so res is the numbers as a list, and this is the working code output:

173 AAPPKAVLKLEPQWINVLQEDSVTLTCRGTHSPESDSIQWFHNGNLIPTHTQPSYRFKANNNDSGEYTCQTGQTSLSDPVHLTVLSEWLVLQTPHLEFQEGETIVLRCHSWKDKPLVKVTFFQNGKSKKFSRSDPNFSIPQANHSHSGDYHCTGNIGYTLYSSKPVTITVQAP Where 173 is the length of the shortened sequence, followed by the sequence.

df sample: 

shortened_mobidb_consensus;sequence
[[45, 45, 'D'], [46, 49, 'C'], [50, 66, 'S'], [67, 101, 'C'], [102, 103, 'S'], [104, 106, 'C'], [107, 108, 'S'], [109, 120, 'C'], [121, 121, 'S'], [122, 123, 'C'], [124, 140, 'S'], [141, 149, 'C'], [150, 176, 'S'], [177, 178, 'C'], [179, 181, 'S'], [182, 194, 'C'], [195, 213, 'S'], [214, 217, 'C']];MGILSFLPVLATESDWADCKSPQPWGHMLLWTAVLFLAPVAGTPAAPPKAVLKLEPQWINVLQEDSVTLTCRGTHSPESDSIQWFHNGNLIPTHTQPSYRFKANNNDSGEYTCQTGQTSLSDPVHLTVLSEWLVLQTPHLEFQEGETIVLRCHSWKDKPLVKVTFFQNGKSKKFSRSDPNFSIPQANHSHSGDYHCTGNIGYTLYSSKPVTITVQAPSSSPMGIIVAVVTGIAVAAIVAAVVALIYCRKKRISALPGYPECREMGETLPEKPANPTNPDEADKVGAENTITYSLLMHPDALEEPDDQNRI
[[1, 1, 'D'], [2, 143, 'S'], [144, 145, 'C']];MGKGKPRGLNSARKLRVHRRNNRWAETTYKKRLLGTAFKSSPFGGSSHAKGIVLEKIGIESKQPNSAIRKCVRVQLIKNGKKVTAFVPNDGCLNFVDENDEVLLAGFGRKGKAKGDIPGVRFKVVKVSGVSLLALWKEKKEKPRS
[[1, 145, 'S']];MGKGKPRGLNSARKLRVHRRNNRWAETTYKKRLLGTAFKSSPFGGSSHAKGIVLEKIGIESKQPNSAIRKCVRVQLIKNGKKVTAFVPNDGCLNFVDENDEVLLAGFGRKGKAKGDIPGVRFKVVKVSGVSLLALWKEKKEKPRS
[[1, 1, 'D'], [2, 2, 'C'], [3, 37, 'S'], [38, 39, 'C'], [40, 40, 'S'], [41, 41, 'C'], [42, 62, 'S'], [63, 65, 'C'], [66, 231, 'S']];MSKNILVLGGSGALGAEVVKFFKSKSWNTISIDFRENPNADHSFTIKDSGEEEIKSVIEKINSKSIKVDTFVCAAGGWSGGNASSDEFLKSVKGMIDMNLYSAFASAHIGAKLLNQGGLFVLTGASAALNRTSGMIAYGATKAATHHIIKDLASENGGLPAGSTSLGILPVTLDTPTNRKYMSDANFDDWTPLSEVAEKLFEWSTNSDSRPTNGSLVKFETKSKVTTWTNL
[[24, 29, 'D'], [30, 91, 'S'], [92, 92, 'D']];MKVSTTALAVLLCTMTLCNQVFSAPYGADTPTACCFSYSRKIPRQFIVDYFETSSLCSQPGVIFLTKRNRQICADSKETWVQEYITDLELNA

Upvotes: 0

Views: 72

Answers (1)

1__
1__

Reputation: 1571

Solution 1:

df = pd.read_csv('stringsample.txt',sep=';',converters={0:ast.literal_eval})

for index, row in df.iterrows():
    new_s = ''
    res = row.shortened_mobidb_consensus
    for item in res:
        new_s += row.sequence[item[0]-1:item[1]]
    df.loc[index,'output'] = new_s

df['output']

0    AAPPKAVLKLEPQWINVLQEDSVTLTCRGTHSPESDSIQWFHNGNL...
1    MGKGKPRGLNSARKLRVHRRNNRWAETTYKKRLLGTAFKSSPFGGS...
2    MGKGKPRGLNSARKLRVHRRNNRWAETTYKKRLLGTAFKSSPFGGS...
3    MSKNILVLGGSGALGAEVVKFFKSKSWNTISIDFRENPNADHSFTI...
4    APYGADTPTACCFSYSRKIPRQFIVDYFETSSLCSQPGVIFLTKRN...
Name: output, dtype: object

Solution 2: (Fixing your code)

df = pd.read_csv('stringsample.txt',sep=';')
shortenedSeq_list =[] 
counter=0
stringstring=[]
for rows in df.itertuples():
    strSeq2 = rows.sequence
    strremove2 = rows.shortened_mobidb_consensus
    res = ast.literal_eval(strremove2)
    new_s = ''
    for item in res:
        new_s += strSeq2[item[0]-1:item[1]]
    stringstring.append(new_s)

stringstring

['AAPPKAVLKLEPQWINVLQEDSVTLTCRGTHSPESDSIQWFHNGNLIPTHTQPSYRFKANNNDSGEYTCQTGQTSLSDPVHLTVLSEWLVLQTPHLEFQEGETIVLRCHSWKDKPLVKVTFFQNGKSKKFSRSDPNFSIPQANHSHSGDYHCTGNIGYTLYSSKPVTITVQAP',
 'MGKGKPRGLNSARKLRVHRRNNRWAETTYKKRLLGTAFKSSPFGGSSHAKGIVLEKIGIESKQPNSAIRKCVRVQLIKNGKKVTAFVPNDGCLNFVDENDEVLLAGFGRKGKAKGDIPGVRFKVVKVSGVSLLALWKEKKEKPRS',
 'MGKGKPRGLNSARKLRVHRRNNRWAETTYKKRLLGTAFKSSPFGGSSHAKGIVLEKIGIESKQPNSAIRKCVRVQLIKNGKKVTAFVPNDGCLNFVDENDEVLLAGFGRKGKAKGDIPGVRFKVVKVSGVSLLALWKEKKEKPRS',
 'MSKNILVLGGSGALGAEVVKFFKSKSWNTISIDFRENPNADHSFTIKDSGEEEIKSVIEKINSKSIKVDTFVCAAGGWSGGNASSDEFLKSVKGMIDMNLYSAFASAHIGAKLLNQGGLFVLTGASAALNRTSGMIAYGATKAATHHIIKDLASENGGLPAGSTSLGILPVTLDTPTNRKYMSDANFDDWTPLSEVAEKLFEWSTNSDSRPTNGSLVKFETKSKVTTWTNL',
 'APYGADTPTACCFSYSRKIPRQFIVDYFETSSLCSQPGVIFLTKRNRQICADSKETWVQEYITDLELNA']

Upvotes: 1

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