E_coli_gff: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Escherichia_coli/reference/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.gff.gz

$ /c/ProgramData/Anaconda3/python

$ winpty  /c/Users/SWCarpentry/Anaconda3/python.exe


### Links

- [Python 3 Quick Tip: The easy way to deal with file paths on Windows, Mac and Linux](https://medium.com/@ageitgey/python-3-quick-tip-the-easy-way-to-deal-with-file-paths-on-windows-mac-and-linux-11a072b58d5f)

### Leseempfehlungen

- [Automate boring stuff with Python](https://automatetheboringstuff.com/)



## Wie es nach dem LC-Workshop weiter geht:
 - Git Bash und Anaconda auf dem eigenen Rechner installieren (gegebenenfalls IT-Abteilung fragen)
 
 - Einen guten Text-Editor finden - ein paar Empfehlungen: 
    1) [PyCharm](https://www.jetbrains.com/pycharm/)
    2) [Spyder](https://www.spyder-ide.org/)
    3) [Atom](https://atom.io/)
    4) [Emacs](https://www.gnu.org/software/emacs/)
    5) [Geany](https://www.geany.org/)
    6) ... [viele mehr](https://en.wikipedia.org/wiki/List_of_text_editors)
 - Lektionen selbstständig reproduzieren
 - kleine alltägliche Aufgabe finden, die man mit Hilfe des Gelernten lösen kann, so das sie automatisch abläuft
 - [HackyHour](https://hackyhour.github.io/Cologne/) organisieren 
 - Bei Problemen melden (wir helfen gerne falls möglich)

gff_data = pd.read_csv(gff_file, 
                       sep="\t", 
                       comment="#",
                      names=["seqid",
                            "source",
                            "type",
                            "start",
                            "end",
                            "score",
                            "strand",
                            "phase",
                            "attributes"])
                            

"https://github.com/foerstner-lab/Bits_and_pieces_for_the_carpentries_workshops/blob/master/python/Expression_data.csv?raw=true"

"https://raw.githubusercontent.com/foerstner-lab/Bits_and_pieces_for_the_carpentries_workshops/master/text_file_examples/Expression_comparison.csv"

gff_files_and_source_urls = {"S_aureus.gff.gz" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/013/425/GCF_000013425.1_ASM1342v1/GCF_000013425.1_ASM1342v1_genomic.gff.gz",
                           "S_typhimurium.gff.gz" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/195/995/GCF_000195995.1_ASM19599v1/GCF_000195995.1_ASM19599v1_genomic.gff.gz",
                           "E_coli.gff.gz":"ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Escherichia_coli/reference/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.gff.gz"}
                           

source_url = "https://raw.githubusercontent.com/foerstner-lab/Bits_and_pieces_for_the_carpentries_workshops/master/text_file_examples/Expression_comparison.csv"
table_file = "Expression_comparison.csv"