How to concatenate only identical file names within two folders to one file?

Question

I have fasta.qz sequence files with identical names, but in two different folders that I need to concatenate (concatenate always those two with identical names only!). The directory structure looks like this:

sequences

**|--folderA**

|  \-- \--MOSA_F_TAC01n.1.fq.gz       
 |  \-- --MOSA_F_TAC08n.rem.1.fq.gz       
 |  \-- --WAIN_N_15m.rem.2.fq.gz       
 |  \-- --MOSA_F_TAC01n.2.fq.gz       
 |  \-- --MOSA_F_TAC08n.rem.2.fq.gz       
 |  \-- --WAIN_N_16m.1.fq.gz       
 |  \-- --MOSA_F_TAC01n.rem.1.fq.gz       
 |  \-- --PAUA_F_16v.1.fq.gz       
 |  \-- --WAIN_N_16m.2.fq.gz       
 |  \-- --MOSA_F_TAC01n.rem.2.fq.gz       
 |  \-- --PAUA_F_16v.2.fq.gz     


**| \--folderB**       
 |  \-- --MOSA_F_TAC01n.1.fq.gz       
 |  \-- --MOSA_F_TAC08n.rem.1.fq.gz       
 |  \-- --WAIN_N_15m.rem.2.fq.gz       
 |  \-- --MOSA_F_TAC01n.2.fq.gz       
 |  \-- --MOSA_F_TAC08n.rem.2.fq.gz       
 |  \-- --WAIN_N_16m.1.fq.gz       
 |  \-- --MOSA_F_TAC01n.rem.1.fq.gz       
 |  \-- --PAUA_F_16v.1.fq.gz       
 |  \-- --WAIN_N_16m.2.fq.gz       
 |  \-- --MOSA_F_TAC01n.rem.2.fq.gz       
 |  \-- --PAUA_F_16v.2.fq.gz   

As you see, the file names are identical (their content is not, i.e., it is complementary thus need to cat). I would like to keep the files' names and concatenate the identical files into one single file with said name (in e.g. a new folder named folderC).

Answer 1

Try something like this:

for FILE in dir1/* ; do
    FILE2=dir2/${FILE#*/}
    if [ -f $FILE2 ] ; then
        cat $FILE $FILE2 > dir3/${FILE#*/}
    fi
done

Where dir1 is one of the source directories, dir2 is the other source directory, and dir3 is the output directory.

Answer 2

I'm afraid its not that easy. The files' "extensions" indicate those are gzipped data that need to be gunzipped before they can be concatenated. Stealing from Christian Gibbons' answer, try

for FILE in dir1/* ; do
    FILE2=dir2/${FILE#*/}
    if [ -f $FILE2 ] ; then
        gunzip -c $FILE $FILE2 | gzip > dir3/${FILE#*/}
    fi
done