CODEWITHSUNDEEP
bash
justaguy
justaguy

Reputation: 3022

bash to search file based on user input and create new file

In the below bash a file is downloaded when the program is opened and then that file is searched based on user input and the result is written to a new file. As of now the file downloads and the user is prompted for the input, but after it is entered nothing happens.

For example, the bash is opened and the download.txt is downloaded, the user then enters the id (NA04520). The id is used to search download.txt and the line is written to match.txt. The code runs but no output result. Eventually, I will search for specific text in the line that id was found in, but I figured getting the search based on user input was a good start. Thank you :).

#!/bin/bash

cd 'C:\Users\cmccabe\Desktop\wget'
wget -O getCSV.txt http://xxx.xx.xxx.xxx/data/getCSV.csv --progress=bar:force 2>&1 | tail -f -n +6 
{
printf "\n\n"
printf "What is the id of the NGS patient: "; read id
     [ -z "$id" ] && printf "\n No ID supplied. Leaving match function." && sleep 2 && return
     [ "$id" = "end" ] && printf "\n Leaving match function." && sleep 2 && return
}


input=$id    
while read -r line
do
case $line in 
    *$id*) 
        echo $line " yes" >> bashgrep.txt
        ;;
    *)
            echo "no"
            ;;
esac
done

Contents of download.txt

 Report,Status,Flows,Library,TF Name,Q10 Mean,Q17 Mean,System SNR,50Q10     Reads,50Q17 Reads,Keypass Reads,TF Key Peak Counts,Total_Num_Reads,Library_50Q10_Reads,Library_100Q10_Reads,Library_200Q10_Reads,Library_Mean_Q10_Length,Library_Q10_Coverage,Library_Q10_Longest_Alignment,Library_Q10_Mapped Bases,Library_Q10_Alignments,Library_50Q17_Reads,Library_100Q17_Reads,Library_200Q17_Reads,Library_Mean_Q17_Length,Library_Q17_Coverage,Library_Q17_Longest_Alignment,Library_Q17_Mapped Bases,Library_Q17_Alignments,Library_50Q20_Reads,Library_100Q20_Reads,Library_200Q20_Reads,Library_Mean_Q20_Length,Library_Q20_Coverage,Library_Q20_Longest_Alignment,Library_Q20_Mapped Bases,Library_Q20_Alignments,Library_Key_Peak_Counts,Library_50Q47_Reads,Library_100Q47_Reads,Library_200Q47_Reads,Library_Mean_Q47_Length,Library_Q47_Coverage,Library_Q47_Longest_Alignment,Library_Q47_Mapped Bases,Library_Q47_Alignments,Library_CF,Library_IE,Library_DR,Library_SNR,Raw Accuracy,Sample,Notes,Run Name,PGM Name,Run Date,Run Directory,Num_Washouts,Num_Dud_Washouts,Num_Washout_Ambiguous,Num_Washout_Live,Num_Washout_Test_Fragment,Num_Washout_Library,Library_Pass_Basecalling,Library_pass_Cafie,Number_Ambiguous,Nubmer_Live,Number_Dud,Number_TF,Number_Lib,Number_Bead,Library_Live,Library_Keypass,TF_Live,TF_Keypass,Keypass_All_Beads,P,s
Auto_user_MOL-95-Epilepsy70_125,Completed,500,hg19,TF_A,93.0,90.0,27.4077550007,27969.0,27031.0,28647.0,93.0,5046334,4861480,4439577,2307648,179,0.0,343,885197150,4942977,4689944,4272916,2213442,177,0.0,341,850800392,4796942,4465846,4082874,2050257,171,0.0,341,804445593,4698861,81.0,4073847,3251302,1186042,143,0.0,319,651683806,4541746,0.515698455274,0.728147709742,0.00734527275199,21.2101955615,99.4,NA04520,NA04520,R_2014_01_14_16_21_42_user_MOL-95-Epilepsy70,MolecularGenetics,2014-01-14 22:21:42+00:00,/results/MolecularGenetics/R_2014_01_14_16_21_42_user_MOL-95-Epilepsy70,0,0,0,0,0,0,0,0,0,9332288,14179,31491,9300797,9346467,0,0,9332288,0,0,"{""variantCaller"": {""hotspots"": {}, ""barcoded"": ""false"", ""Target Regions"": ""Epilepsy70"", ""Trim Reads"": true, ""Target Loci"": ""Not using"", ""variants"": {""no_call"": 0, ""homo_snps"": 50, ""het_snps"": 104, ""other"": 0, ""variants"": 163, ""het_indels"": 3, ""homo_indels"": 6}, ""Configuration"": ""Germ Line - Low Stringency"", ""Aligned Reads"": ""R_2014_01_14_16_21_42_user_MOL-95-Epilepsy70"", ""Library Type"": ""AmpliSeq""}}","{""FastqCreator"": {}}","{""coverageAnalysis"": {""Bases in target regions"": ""268545"", ""Amplicons with at least 1 read"": ""99.80%"", ""barcoded"": ""false"", ""Target base coverage at 100x"": ""97.72%"", ""Amplicons with at least 500 reads"": ""95.42%"", ""Total assigned amplicon reads"": ""4879939"", ""Reference (File)"": ""hg19"", ""Total aligned base reads"": ""884883559"", ""Target base coverage at 20x"": ""98.82%"", ""Number of amplicons"": ""1507"", ""Target bases with no strand bias"": ""84.70%"", ""Percent reads on target"": ""97.44%"", ""Amplicons with at least 100 reads"": ""98.08%"", ""Average base coverage depth"": ""3149"", ""Average reads per amplicon"": ""3238"", ""Using"": ""All Mapped Reads"", ""Amplicons reading end-to-end"": ""80.76%"", ""Non-duplicate"": """", ""Uniquely mapped"": ""No"", ""Targeted Regions"": ""Epilepsy70"", ""Uniformity of base coverage"": ""93.35%"", ""Targetted regions"": ""/results/uploads/BED/42/hg19/merged/plain/Epilepsy70.bed"", ""Target padding"": ""0"", ""Amplicons with at least 20 reads"": ""99.14%"", ""Number of mapped reads"": ""5007953"", ""Percent assigned amplicon reads"": ""97.44%"", ""Amplicons

Upvotes: 1

Views: 52

Answers (1)

Jahid
Jahid

Reputation: 22438

Change the while loop to:

while IFS= read -r line
do
case "$line" in 
    *$id*) 
        echo "$line" >> bashgrep.txt
        echo "yes"
#Assumed you want only $line to go to the file and print yes to stdout
        ;;
    *)
        echo "no"
        ;;
esac
done <download.txt 
#change it to the name of the file downloaded. 
#Your posted code seems to download getCSV.txt

Upvotes: 1

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