Any python script to merge files

Question

[BehMah]

Hi Guys,

I have a list of genes and their RPMs for some samples (bed file) and wanna merge all genes and their RPMs from bed files into one new bed file (for differential expression analysis). Can anybody please give me a python script to do it?

Really thanks

Answer 1

[BehMah]

its like the following: if gene_id in file a.txt and b.txt is identical add value1 into outfile

A.txt: gene_id value1

B.txt: gene_id value1

output: gene_id value1(A.txt) value1(B.txt)

Answer 2

[shenwei356]

csvtk join of csvtk. supposing a.txt and b.txt are tab-delimited files.

csvtk join -H -t -f gene_id a.tsv b.tsv

Answer 3

[BehMah]

hi shenwei356,

Thanks for your reply and this useful tool. just was wondering if it is still doable to run it for 40 input files? and also *.txt files have multiple tabs in addition to value 1, then can I specify only value1 ?

[shenwei356]

Please reply an answer by clicking ADD COMMENT below the answer.

csvtk join supports joining 2+ files.

If you have more columns, you can firstly retrieve the columns gene_id and value to a separated files, and then join.

Does the file has column names? If so, you can cut by column names (i.e., GENE, VALUE..), if not, switch flag -H on and use column fields (i.e., 1, 2...)

for f in *.txt; do \
    csvtk cut -H -t -f "1,2" "$f" > "$f.gene2value.tsv; \
done

Then join:

csvtk join -H -t -f 1 *.gene2value.tsv

[BehMah]

Thanks do much shenwei356. When I run the first script it retrieve only fist line of the field 1,2. seems like it doesn't do any loop ??